[English] 日本語
![](img/lk-miru.gif)
- PDB-5l2g: Solution Structure of a DNA Dodecamer with 5-methylcytosine at th... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5l2g | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th Position | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Drew-Dickerson / non-canonical / modified DNA / methylated DNA / epigenetics / CpG site | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | SOLUTION NMR / simulated annealing | ![]() Miears, H.L. / Hoppins, J.J. / Gruber, D.R. / Kasymov, R.D. / Johnson, E.C. / Zharkov, D.O. / Smirnov, S.L. | Funding support | | ![]()
![]() ![]() Title: Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation. Authors: Gruber, D.R. / Toner, J.J. / Miears, H.L. / Shernyukov, A.V. / Kiryutin, A.S. / Lomzov, A.A. / Endutkin, A.V. / Grin, I.R. / Petrova, D.V. / Kupryushkin, M.S. / Yurkovskaya, A.V. / Johnson, ...Authors: Gruber, D.R. / Toner, J.J. / Miears, H.L. / Shernyukov, A.V. / Kiryutin, A.S. / Lomzov, A.A. / Endutkin, A.V. / Grin, I.R. / Petrova, D.V. / Kupryushkin, M.S. / Yurkovskaya, A.V. / Johnson, E.C. / Okon, M. / Bagryanskaya, E.G. / Zharkov, D.O. / Smirnov, S.L. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 143.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 115.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 329 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 386.6 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l06C ![]() 5trnC ![]() 5uz1C ![]() 5uz2C ![]() 5uz3C ![]() 6alsC ![]() 6altC ![]() 6aluC C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: DNA chain | Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-
Sample preparation
Details | Type: solution Contents: 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3'), 100% D2O Label: 5metC9 / Solvent system: 100% D2O | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||
Sample conditions |
|
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
---|
-
Processing
NMR software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 6 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 18 / Conformers submitted total number: 9 |